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comparison kodoja_search.xml @ 0:18fe33eb7775 draft

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Uploaded kodoja_search.py v0.0.3 wrapper. https://github.com/abaizan/kodoja_galaxy/commit/55004d41a9c0750b2543f394594ee58cc4426609
author peterjc
date Wed, 14 Mar 2018 12:46:57 -0400
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1 <tool id="kodoja_search" name="Kodoja database search" version="0.0.0">
2 <description>identify viruses from plant RNA sequencing data</description>
3 <requirements>
4 <requirement type="package" version="0.0.3">kodoja</requirement>
5 </requirements>
6 <version_command>kodoja_search.py --version</version_command>
7 <command detect_errors="exit_code"><![CDATA[
8 kodoja_search.py
9
10 --kraken_db '${kraken_db.fields.path}'
11 --kaiju_db '${kaiju_db.fields.path}'
12
13 #if $single_paired.single_paired_selector == 'yes'
14 #if $forward_input.is_of_type( 'fastq' ):
15 --data_format fastq
16 #else:
17 --data_format fasta
18 #end if
19 --read1 '${single_paired.forward_input}'
20 --read2 '${single_paired.reverse_input}'
21 #else:
22 #if $single_paired.input_sequences.is_of_type('fastq')
23 --data_format fastq
24 #else:
25 --data_format fasta
26 #end if
27 --read1 '${single_paired.input_sequences}'
28 #end if
29
30 ## TODO:
31 ## -m min_trim
32 ## -a trim_adapt
33 ## -q kraken_quick
34 ## -p kraken_preload
35 ## -c kaiju_score
36 ## -l kaiju_minlen
37 ## -i kaiju_mismatch
38
39 ## We'll capture predictably named output files from here:
40 -o .
41 &&
42 mv ./virus_table.txt '$combined_table'
43 ]]></command>
44 <inputs>
45 <param label="Select a Kraken database" name="kraken_db" type="select">
46 <options from_data_table="kraken_databases">
47 <validator message="No Kraken database is available" type="no_options" />
48 </options>
49 </param>
50 <param label="Select a Kaiju database" name="kaiju_db" type="select">
51 <options from_data_table="kaiju_databases">
52 <validator message="No Kaiju database is available" type="no_options" />
53 </options>
54 </param>
55 <conditional name="single_paired">
56 <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">
57 <!-- TODO?
58 <option value="collection">Collection</option>
59 -->
60 <option value="yes">Paired</option>
61 <option selected="True" value="no">Single</option>
62 </param>
63 <when value="yes">
64 <param format="fasta,fastq" name="forward_input" type="data" label="Forward strand" help="FASTA or FASTQ dataset"/>
65 <param format="fasta,fastq" name="reverse_input" type="data" label="Reverse strand" help="FASTA or FASTQ dataset"/>
66 </when>
67 <when value="no">
68 <param format="fasta,fastq" label="Input sequences" name="input_sequences" type="data" help="FASTA or FASTQ datasets"/>
69 </when>
70 </conditional>
71 </inputs>
72 <outputs>
73 <data name="combined_table" format="tabular" label="Kodoja species report for ${on_string}" />
74 </outputs>
75 <tests>
76 <test>
77 <param name="kraken_db" value="kraken3viruses" />
78 <param name="kaiju_db" value="kaiju3viruses" />
79 <param name="single_paired_selector" value="no" />
80 <param name="input_sequences" value="testData_1.fastq" ftype="fastq" />
81 <output name="combined_table" file="virus_table_SE_fastq.tabular" ftype="tabular" />
82 </test>
83 <test>
84 <param name="kraken_db" value="kraken3viruses" />
85 <param name="kaiju_db" value="kaiju3viruses" />
86 <param name="single_paired_selector" value="yes" />
87 <param name="forward_input" value="testData_1.fastq" ftype="fastq" />
88 <param name="reverse_input" value="testData_2.fastq" ftype="fastq" />
89 <output name="combined_table" file="virus_table_PE_fastq.tabular" ftype="tabular" />
90 </test>
91 <test>
92 <param name="kraken_db" value="kraken3viruses" />
93 <param name="kaiju_db" value="kaiju3viruses" />
94 <param name="single_paired_selector" value="yes" />
95 <param name="forward_input" value="testData_1.fasta" ftype="fasta" />
96 <param name="reverse_input" value="testData_2.fasta" ftype="fasta" />
97 <output name="combined_table" file="virus_table_PE_fasta.tabular" ftype="tabular" />
98 </test>
99 </tests>
100 <help><![CDATA[
101 Kodoja is a tool intended to identify viral sequences in a
102 FASTQ/FASTA sequencing run by matching them against both
103 Kraken and Kaiju databases.
104
105 The main output is a five column tab-separated table as follows
106 (tabular format in Galaxy):
107
108 1. Species name
109 2. Species NCBI taxonomy identifier (TaxID)
110 3. Number of reads assigned by *either* Kraken or Kaiju to this species
111 4. Number of Reads assigned by *both* Kraken and Kaiju to this species
112 5. Genus name
113 6. Number of reads assigned by *either* Kraken or Kaiju to this genus
114 7. Number of reads assigned by *both* Kraken and Kaiju to this genus
115
116 For example,
117
118 ================================== ============= ================= ============================= ========== =============== ===========================
119 Species Species TaxID Species sequences Species sequences (stringent) Genus Genus sequences Genus sequences (stringent)
120 ---------------------------------- ------------- ----------------- ----------------------------- ---------- --------------- ---------------------------
121 Cassava brown streak virus 137758 45 45 Ipomovirus
122 Ugandan cassava brown streak virus 946046 28 28 Ipomovirus
123 Tobacco etch virus 12227 21 19 Potyvirus
124 ================================== ============= ================= ============================= ========== =============== ===========================
125
126 This is the command line tool's help::
127
128 usage: kodoja_search.py [-h] [--version] -o OUTPUT_DIR -d1 KRAKEN_DB -d2
129 KAIJU_DB -r1 READ1 [-r2 READ2] [-f DATA_FORMAT]
130 [-t THREADS] [-s] [-m TRIM_MINLEN] [-a TRIM_ADAPT]
131 [-q KRAKEN_QUICK] [-p] [-c KAIJU_SCORE]
132 [-l KAIJU_MINLEN] [-i KAIJU_MISMATCH]
133
134 Kodoja
135
136 optional arguments:
137 -h, --help show this help message and exit
138 --version show program's version number and exit
139 -o OUTPUT_DIR, --output_dir OUTPUT_DIR
140 Output directory path, required
141 -d1 KRAKEN_DB, --kraken_db KRAKEN_DB
142 Kraken database path, required
143 -d2 KAIJU_DB, --kaiju_db KAIJU_DB
144 Kaiju database path, required
145 -r1 READ1, --read1 READ1
146 Read 1 file path, required
147 -r2 READ2, --read2 READ2
148 Read 2 file path
149 -f DATA_FORMAT, --data_format DATA_FORMAT
150 Sequence data format
151 -t THREADS, --threads THREADS
152 Number of threads
153 -s, --host_subset Subset host sequences before Kaiju
154 -m TRIM_MINLEN, --trim_minlen TRIM_MINLEN
155 Trimmomatic minimum length
156 -a TRIM_ADAPT, --trim_adapt TRIM_ADAPT
157 Illumina adapter sequence file
158 -q KRAKEN_QUICK, --kraken_quick KRAKEN_QUICK
159 Number of minium hits by Kraken
160 -p, --kraken_preload Kraken preload database
161 -c KAIJU_SCORE, --kaiju_score KAIJU_SCORE
162 Kaju alignment score
163 -l KAIJU_MINLEN, --kaiju_minlen KAIJU_MINLEN
164 Kaju minimum length
165 -i KAIJU_MISMATCH, --kaiju_mismatch KAIJU_MISMATCH
166 Kaju allowed mismatches
167
168 ]]></help>
169 <citations>
170 <citation type="bibtex">
171 @misc{githubkodoja,
172 author = {Baizan Edge, Amanda},
173 year = {2018},
174 title = {Kodoja},
175 publisher = {GitHub},
176 journal = {GitHub repository},
177 url = {https://github.com/abaizan/kodoja},
178 }</citation>
179 </citations>
180 </tool>